converting from docker to singuarity

[rcwelsh]

Hi, I'm on a freshly installed ubuntu 20.04.5 and wanting to convert fmriprep 22.1.1 from docker to singularity. I used the command:

singularity build /home/Software/fmriPrep/Singularity/fmriprep-22.1.1.simg docker://nipreps/fmriprep:22.1.1

per the instructions from https://www.nipreps.org/apps/singularity/ due to having singularity 3.5.3 installed.

It fails, here is the output of the conversion command:

INFO:    Starting build...
Getting image source signatures
Copying blob 345e3491a907 done
Copying blob 57671312ef6f done
Copying blob 5e9250ddb7d0 done
Copying blob f6495e0624c3 done
Copying blob 1a6817b82c0a done
Copying blob bbb790451e4e done
Copying blob 741d900bbd0b done
Copying blob c8056b469e9d done
Copying blob 013807c18928 done
Copying blob 7bc2014d2c4c done
Copying blob 528612794565 done
Copying blob 9e1c838547f7 done
Copying blob cc44be6452b1 done
Copying blob 2582d5c2dc90 done
Copying blob cab6f6836004 done
Copying blob ea3f8bb1e5c5 done
Copying blob 391c03a3659c done
Copying blob 5d80d1c671f5 done
Copying blob 37084dba296f done
Copying blob dd56ae478ab0 done
Copying blob 2225e96bee80 done
Copying blob 385f142c0c89 done
Copying blob 3b106d8705c8 done
Copying blob eac70a08e0e9 done
Copying config e5bcd2759d done
Writing manifest to image destination
Storing signatures
2023/02/13 22:35:39  info unpack layer: sha256:345e3491a907bb7c6f1bdddcf4a94284b8b6ddd77eb7d93f09432b17b20f2bbe
2023/02/13 22:35:40  info unpack layer: sha256:57671312ef6fdbecf340e5fed0fb0863350cd806c92b1fdd7978adbd02afc5c3
2023/02/13 22:35:40  info unpack layer: sha256:5e9250ddb7d0fa6d13302c7c3e6a0aa40390e42424caed1e5289077ee4054709
2023/02/13 22:35:40  info unpack layer: sha256:f6495e0624c31b9b4513b9d3f55faebe7ca84a03ff31dedd74ced4ba0a590097
2023/02/13 22:35:44  info unpack layer: sha256:1a6817b82c0a9124da3863a82afc54bc3e7982461d0dae671501df67657d704a
2023/02/13 22:35:44  info unpack layer: sha256:bbb790451e4eab04c22cde38f9aa48818a023a96a988ad133d44e1d6a436d115
2023/02/13 22:36:08  info unpack layer: sha256:741d900bbd0b497e467f054a0f1397f1547119d60e375af51c6873758f5d6ec5
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/ApplyXFM} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Bet} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/ConcatXFM} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Fast} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Fdt} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Feat} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Featquery} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Flirt} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Fsl_prepare_fieldmap} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Glm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/InvertXFM} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Make_flobs} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Melodic} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Nudge} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Pnm} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Possum} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Renderhighres} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Renderstats} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:08  warn rootless{opt/fsl-6.0.5.1/bin/Susan} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:09  warn rootless{opt/fsl-6.0.5.1/bin/fsl} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:09  warn rootless{opt/fsl-6.0.5.1/bin/fsl_gui} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:11  warn rootless{opt/fsl-6.0.5.1/lib/libOSMesa.so} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:11  warn rootless{opt/fsl-6.0.5.1/lib/libOSMesa.so.6} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:11  warn rootless{opt/fsl-6.0.5.1/lib/libOSMesa16.so} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:11  warn rootless{opt/fsl-6.0.5.1/lib/libOSMesa16.so.6} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:11  warn rootless{opt/fsl-6.0.5.1/lib/libOSMesa32.so} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:11  warn rootless{opt/fsl-6.0.5.1/lib/libOSMesa32.so.6} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:11  warn rootless{opt/fsl-6.0.5.1/lib/libQVTK.so} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
2023/02/13 22:36:11  warn rootless{opt/fsl-6.0.5.1/lib/libQVTK.so.5.0} ignoring (usually) harmless EPERM on setxattr "user.rootlesscontainers"
FATAL:   While performing build: packer failed to pack: while unpacking tmpfs: error unpacking rootfs: unpack layer: unpack entry: opt/fsl-6.0.5.1/lib/libopenblaso-r0.3.3.so: write /tmp/rootfs-95a6ea18-ac31-11ed-a954-3cecefb980c0/opt/fsl-6.0.5.1/lib/libopenblaso-r0.3.3.so: no space left on device

Current disk usage is :

df -h
Filesystem      Size  Used Avail Use% Mounted on
udev           1008G     0 1008G   0% /dev
tmpfs           202G   12M  202G   1% /run
/dev/nvme4n1p2   49G   39G  8.4G  82% /
tmpfs          1008G     0 1008G   0% /dev/shm
tmpfs           5.0M     0  5.0M   0% /run/lock
tmpfs          1008G     0 1008G   0% /sys/fs/cgroup
/dev/nvme5n1p1  1.9T   28K  1.8T   1% /mnt/data0
/dev/nvme3n1p1   12T  3.4M   12T   1% /nyx4
/dev/nvme2n1p1   12T  155G   12T   2% /nyx3
/dev/nvme1n1p1   12T  3.4M   12T   1% /nyx2
/dev/nvme0n1p1   12T  175G   12T   2% /nyx1
/dev/nvme4n1p1  511M  6.1M  505M   2% /boot/efi
/dev/nvme4n1p4  1.8T   84G  1.7T   5% /home
/dev/loop1       64M   64M     0 100% /snap/core20/1778
/dev/loop2       92M   92M     0 100% /snap/lxd/24061
/dev/loop3       70M   70M     0 100% /snap/lxd/19188
/dev/loop4       56M   56M     0 100% /snap/core18/2667
/dev/loop5       50M   50M     0 100% /snap/snapd/17950
tmpfs           202G  8.0K  202G   1% /run/user/122
tmpfs           202G  8.0K  202G   1% /run/user/1001
/dev/loop6       56M   56M     0 100% /snap/core18/2679
/dev/loop0       64M   64M     0 100% /snap/core20/1822

[effigies]

Apologies for missing this. According to apptainer/singularity#1165, you may want to use --sandbox.